Default Question about reconsideration strategy

I am going to move to a new domain after a google penalty. I will de index my pages and place a note on the homepage with the new address.

My question is - if i continue removing bad links and disavow the rest and file a reconsideration, once the site gets revoked will it help me or hurt me to 301 redirect to the new site?
My thought is that once the old site is cleared its OK to 301. Also, there still will be good links going to the old homepage and if I 301 redirect i may get credit for them.

You are correct. But make sure that you recieve a reply from Google on WMT stating that your request have been processed or went through.
If your site no longer has any manual action messages on WebMaster Tools, you are good to use that URL - even for 301 redirect to get the link value out of it

I agree with Avinash.....be sure to monitor your WMT account and wait until you can confirm that the old site's penalty has been lifted. Manually confirm this by checking the SERPs and in Google Analytics. If all is well, the 301 redirect from old domain to new should be fine.